Re: [PyMOL] Rotation of a Protein
Create two new molecules from the originial. then import rotkit *rotateline Pos1=**atomcoordM1**, Pos2=atomcoordM2, degangle=60, molecule=dim1* 2011/10/9 kanika sharma ksharma...@gmail.com I need to rotate the second unit of the dimeric protein on the line joining their center of masses. rotate it at a atep of 60 degrees till 240 degree.. 2011/10/8 Troels Emtekær Linnet tlin...@gmail.com If you need rotations around an line, instead of axis, check out http://www.pymolwiki.org/index.php/Rotkit Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/ 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/10/7 kanika sharma ksharma...@gmail.com Hello everyone, I Have a protein with 2 chains. I have to rotate the second chain of the protein by 60,120,180,240 degrees each. Is there a script in PyMol that can do that? Best, Kanika -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] How did they generate this figure
Hi, The picture in http://www.pymol.org/ is gorgeous, just wonder how did it produce such purple cloud effect? Thanks for any hint. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Setting-Error: type read mismatch (float) -1
Hi, I met the following error after recently update some (other) package. once start pymol, it would show lines of the same Setting-Error: type read mismatch (float) -1 later, for every move I took in using it, it would show: Setting-Error: type read mismatch (int) 667 except those Setting-Error, other things function as usual. Thanks, -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Setting-Error: type read mismatch (float) -1
On Sun, Oct 9, 2011 at 10:50 PM, lina lina.lastn...@gmail.com wrote: Hi, I met the following error after recently update some (other) package. once start pymol, it would show lines of the same Setting-Error: type read mismatch (float) -1 later, for every move I took in using it, it would show: Setting-Error: type read mismatch (int) 667 except those Setting-Error, other things function as usual. Still something abnormal. When I tried to write session, it's terminated and showed: Save: Please wait -- writing session file... Segmentation fault Thanks, -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Setting-Error: type read mismatch (float) -1
Hi Lina, Can you tell more? What version are you using, what system are you on, do you use a .pymolrc, and what exactly do you do? Cheers, Tsjerk On Oct 9, 2011 5:05 PM, lina lina.lastn...@gmail.com wrote: On Sun, Oct 9, 2011 at 10:50 PM, lina lina.lastn...@gmail.com wrote: Hi, I met the followi... Still something abnormal. When I tried to write session, it's terminated and showed: Save: Please wait -- writing session file... Segmentation fault Thanks, -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Setting-Error: type read mismatch (float) -1
On Oct 10, 2011, at 1:04, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Can you tell more? What version are you using, what system are you on, do you use a .pymolrc, and what exactly do you do? Version 1.4. Debian amd64 I did use .pymolrc. Please kindly notice the problem just recent two days showed up. The .pymolrc has been used for a while. Today I reinstalled the pymol. Still the same. Do you think it's related to the .pymolrc? Right now I'm not in front of computer. Later (now is 1:40 am here, probably 8 or 9 hours later) I can remove the .pymolrc and test. Actually I suspected It might due to the update of some package in my box. But I have no clue about how to check further. Thanks. Cheers, Tsjerk On Oct 9, 2011 5:05 PM, lina lina.lastn...@gmail.com wrote: On Sun, Oct 9, 2011 at 10:50 PM, lina lina.lastn...@gmail.com wrote: Hi, I met the followi... Still something abnormal. When I tried to write session, it's terminated and showed: Save: Please wait -- writing session file... Segmentation fault Thanks, -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Setting-Error: type read mismatch (float) -1
Hey Lina, It most likely is a consequence of the update. But the error comes from the settings code, so I assumed that you set some settings at startup, which brings a .pymolrc in mind. Not loading that file would then solve it, although the problem is probably more fundamental, and I would suspect you'd get an error like that when just setting some setting in Pymol. If you can give more information regarding the modules that were updated, it would be very helpful. Otherwise, I'm rather clueless... Cheers, Tsjerk On Sun, Oct 9, 2011 at 7:42 PM, lina lina.lastn...@gmail.com wrote: On Oct 10, 2011, at 1:04, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Can you tell more? What version are you using, what system are you on, do you use a .pymolrc, and what exactly do you do? Version 1.4. Debian amd64 I did use .pymolrc. Please kindly notice the problem just recent two days showed up. The .pymolrc has been used for a while. Today I reinstalled the pymol. Still the same. Do you think it's related to the .pymolrc? Right now I'm not in front of computer. Later (now is 1:40 am here, probably 8 or 9 hours later) I can remove the .pymolrc and test. Actually I suspected It might due to the update of some package in my box. But I have no clue about how to check further. Thanks. Cheers, Tsjerk On Oct 9, 2011 5:05 PM, lina lina.lastn...@gmail.com wrote: On Sun, Oct 9, 2011 at 10:50 PM, lina lina.lastn...@gmail.com wrote: Hi, I met the followi... Still something abnormal. When I tried to write session, it's terminated and showed: Save: Please wait -- writing session file... Segmentation fault Thanks, -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Setting-Error: type read mismatch (float) -1
On Mon, Oct 10, 2011 at 2:58 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Lina, It most likely is a consequence of the update. But the error comes from the settings code, so I assumed that you set some settings at startup, which brings a .pymolrc in mind. Not loading that file would Right now I just simply removed the .pymolrc Problem is still the same with Detected OpenGL version 2.0 or greater. Shaders available. PyMOLShader_NewFromFile-Error: Unable to open file '/usr/share/pymol/data/shaders/default.vs' PYMOL_PATH='/usr/share/pymol' PyMOLShader_NewFromFile-Warning: default shader files not found, loading from memory. PyMOLShader_NewFromFile-Error: Unable to open file '/usr/share/pymol/data/shaders/volume.vs' PYMOL_PATH='/usr/share/pymol' PyMOLShader_NewFromFile-Warning: volume shader files not found, loading from memory. Detected GLSL version 4.10. Detected 8 CPU cores. Enabled multithreaded rendering. Setting-Error: type read mismatch (float) -1 Recently I guess I updated lots of package, the detailed updated package in the recent four days includes: Start-Date: 2011-10-07 21:05:49 Install: libnl3:amd64 (3.0-2, automatic) Upgrade: libreoffice-style-galaxy:amd64 (3.4.3-1, 3.4.3-3), libplist1:amd64 (1.6 -2, 1.6-2+b1), libreoffice-draw:amd64 (3.4.3-1, 3.4.3-3), liblcms1:amd64 (1.19.d fsg-1, 1.19.dfsg-1+b1), gnome-session-bin:amd64 (2.30.2-3+sid1, 2.30.2-3+sid2), python-minimal:amd64 (2.6.7-3, 2.7.2-7), libreoffice-impress:amd64 (3.4.3-1, 3.4 .3-3), libimobiledevice2:amd64 (1.1.1-2, 1.1.1-2+b1), apache2-mpm-worker:amd64 ( 2.2.20-1, 2.2.21-1), pymol:amd64 (1.4.1-1, 1.4.1-1+b1), gnome-session:amd64 (2.3 0.2-3+sid1, 2.30.2-3+sid2), libpolkit-gtk-1-0:amd64 (0.102-1, 0.102-2), gnome-se ssion-common:amd64 (2.30.2-3+sid1, 2.30.2-3+sid2), libavogadro1:amd64 (1.0.3-1+b 1, 1.0.3-1+b2), python-all:amd64 (2.6.7-3, 2.7.2-7), ttf-opensymbol:amd64 (2.4.3 +LibO3.4.3-1, 2.4.3+LibO3.4.3-3), python-dev:amd64 (2.6.7-3, 2.7.2-7), libreoffi ce-report-builder-bin:amd64 (3.4.3-1, 3.4.3-3), liblcms1-dev:amd64 (1.19.dfsg-1, 1.19.dfsg-1+b1), libfcgi-perl:amd64 (0.73-2, 0.74-1), apache2-utils:amd64 (2.2. 20-1, 2.2.21-1), libreoffice-math:amd64 (3.4.3-1, 3.4.3-3), apache2:amd64 (2.2.2 0-1, 2.2.21-1), libreoffice-common:amd64 (3.4.3-1, 3.4.3-3), python-avogadro:amd 64 (1.0.3-1+b1, 1.0.3-1+b2), apache2.2-common:amd64 (2.2.20-1, 2.2.21-1), uno-li bs3:amd64 (3.4.3-1, 3.4.3-3), deskbar-applet:amd64 (2.32.0-1+b2, 2.32.0-1+b3), p ython-uno:amd64 (3.4.3-1, 3.4.3-3), python:amd64 (2.6.7-3, 2.7.2-7), sudo:amd64 (1.8.2-1, 1.8.2-2), libwpd-0.9-9:amd64 (0.9.3-1, 0.9.3-2), apache2.2-bin:amd64 ( 2.2.20-1, 2.2.21-1), policykit-1-gnome:amd64 (0.102-1, 0.102-2), avogadro:amd64 (1.0.3-1+b1, 1.0.3-1+b2), openoffice.org:amd64 (3.4.0~ooo340m1-3, 3.4.0~ooo340m1 -5), wpasupplicant:amd64 (0.7.3-3, 0.7.3-4), libtotem-plparser17:amd64 (2.32.5-2 , 2.32.6-1), ure:amd64 (3.4.3-1, 3.4.3-3), libreoffice-base-core:amd64 (3.4.3-1, 3.4.3-3), libreoffice-base:amd64 (3.4.3-1, 3.4.3-3), libreoffice:amd64 (3.4.3-1 , 3.4.3-3), libreoffice-calc:amd64 (3.4.3-1, 3.4.3-3), libpq5:amd64 (9.1.0-1, 9. 1.1-1), libreoffice-officebean:amd64 (3.4.3-1, 3.4.3-3), libreoffice-emailmerge: amd64 (3.4.3-1, 3.4.3-3), python-all-dev:amd64 (2.6.7-3, 2.7.2-7), libreoffice-j ava-common:amd64 (3.4.3-1, 3.4.3-3), libreoffice-filter-mobiledev:amd64 (3.4.3-1 , 3.4.3-3), pdb2pqr:amd64 (1.7-2, 1.7-2+b1), libreoffice-filter-binfilter:amd64 (3.4.3-1, 3.4.3-3), libjs-jquery:amd64 (1.6.2-1, 1.6.4-1), libreoffice-core:amd6 4 (3.4.3-1, 3.4.3-3), libreoffice-writer:amd64 (3.4.3-1, 3.4.3-3) End-Date: 2011-10-07 21:15:12 Start-Date: 2011-10-07 23:59:10 Upgrade: python3-minimal:amd64 (3.2-3, 3.2.2~rc1-2), python3-dev:amd64 (3.2-3, 3 .2.2~rc1-2), python3-doc:amd64 (3.2-3, 3.2.2~rc1-2), python3.2-minimal:amd64 (3. 2.1~rc1-1, 3.2.2~rc1-1), libpython3.2:amd64 (3.2.1~rc1-1, 3.2.2~rc1-1), python3. 2:amd64 (3.2.1~rc1-1, 3.2.2~rc1-1), python3.2-examples:amd64 (3.2.1~rc1-1, 3.2.2 ~rc1-1), python3:amd64 (3.2-3, 3.2.2~rc1-2), idle3:amd64 (3.2-3, 3.2.2~rc1-2), p ython3.2-dev:amd64 (3.2.1~rc1-1, 3.2.2~rc1-1), python3.2-doc:amd64 (3.2.1~rc1-1, 3.2.2~rc1-1), python3-examples:amd64 (3.2-3, 3.2.2~rc1-2) End-Date: 2011-10-08 00:00:57 Start-Date: 2011-10-08 16:17:23 Upgrade: libatk1.0-0:amd64 (2.0.1-2, 2.2.0-1), mgltools-pybabel:amd64 (1.5.6~rc1 +cvs.20110617-1, 1.5.6~rc2+cvs.20110926-1), mgltools-webservices:amd64 (1.5.6~rc 1+cvs.20110703-1, 1.5.6~rc2+cvs.20110926-1), libatk1.0-data:amd64 (2.0.1-2, 2.2. 0-1), mgltools-volume:amd64 (1.5.6~rc1+cvs.20110617-1, 1.5.6~rc2+cvs.20110926-1) , mgltools-mglutil:amd64 (1.5.6~rc1+cvs.20110617-1, 1.5.6~rc2+cvs.20110926-1), l ibtdb1:amd64 (1.2.9-3, 1.2.9-4+b1), mgltools-scenario2:amd64 (1.5.6~rc1+cvs.2011 0617-1, 1.5.6~rc2+cvs.20110926-1), infernal:amd64 (1.0.2-1, 1.0.2-2), libfuse2:a md64 (2.8.5-5, 2.8.6-1), autodocktools:amd64 (1.5.6~rc1+cvs.20110617-1, 1.5.6~rc 2+cvs.20110926-1), mgltools-viewerframework:amd64 (1.5.6~rc1+cvs.20110617-2, 1.5
Re: [PyMOL] Setting-Error: type read mismatch (float) -1
On Mon, Oct 10, 2011 at 2:58 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Lina, It most likely is a consequence of the update. But the error comes Hi Tsjerk, Right now I downgrade the pymol from 1.4.1-1+b1 to 1.4.1-1. It works. I was kinda of lazy sometimes, should have carefully checked earlier. But, which problem cause the version 1.4.1-1+b1 not functional well I still don't know. (http://packages.debian.org/wheezy/pymol) Thanks, lina from the settings code, so I assumed that you set some settings at startup, which brings a .pymolrc in mind. Not loading that file would then solve it, although the problem is probably more fundamental, and I would suspect you'd get an error like that when just setting some setting in Pymol. If you can give more information regarding the modules that were updated, it would be very helpful. Otherwise, I'm rather clueless... Cheers, Tsjerk On Sun, Oct 9, 2011 at 7:42 PM, lina lina.lastn...@gmail.com wrote: On Oct 10, 2011, at 1:04, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lina, Can you tell more? What version are you using, what system are you on, do you use a .pymolrc, and what exactly do you do? Version 1.4. Debian amd64 I did use .pymolrc. Please kindly notice the problem just recent two days showed up. The .pymolrc has been used for a while. Today I reinstalled the pymol. Still the same. Do you think it's related to the .pymolrc? Right now I'm not in front of computer. Later (now is 1:40 am here, probably 8 or 9 hours later) I can remove the .pymolrc and test. Actually I suspected It might due to the update of some package in my box. But I have no clue about how to check further. Thanks. Cheers, Tsjerk On Oct 9, 2011 5:05 PM, lina lina.lastn...@gmail.com wrote: On Sun, Oct 9, 2011 at 10:50 PM, lina lina.lastn...@gmail.com wrote: Hi, I met the followi... Still something abnormal. When I tried to write session, it's terminated and showed: Save: Please wait -- writing session file... Segmentation fault Thanks, -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
